Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF.

Sin Yi Lee,Jie Yan,Peter Dröge,Ci Ji Lim

doi:10.1038/srep18146

Abstract

The bacterial nucleoid, a bacterial genome packed by nucleoid binding proteins, forms the physical basis for cellular processes such as gene transcription and DNA replication. Bacteria need to dynamically modulate their nucleoid structures at different growth phases and in response to environmental changes. At the nutrients deficient stationary phase, DNA-binding proteins from starved cells (Dps) and Integration host factors (IHF) are the two most abundant nucleoid associated proteins in E. coli. Yet, it remains unclear how the nucleoid architecture is controlled by the interplay between these two proteins, as well as the nucleoid’s response to environmental changes. This question is addressed here using single DNA manipulation approach. Our results reveal that the two proteins are differentially selected for DNA binding, which can be tuned by changing environmental factors over physiological ranges including KCl (50–300 mM), MgCl2 (0–10 mM), pH (6.5–8.5) and temperature (23–37 °C). Increasing pH and MgCl2 concentrations switch from Dps-binding to IHF-binding. Stable Dps-DNA and IHF-DNA complexes are insensitive to temperature changes for the range tested. The environment dependent selection between IHF and Dps results in different physical organizations of DNA. Overall, our findings provide important insights into E. coli nucleoid architecture.

Highlights

Bacteria have a genomic DNA with a contour length that can be in the order of millimetre range (e.g. E. coli, Salmonella, etc)
Many studies have focused on understanding the nucleoid architecture in the exponential growth phase, where nucleoid is organized by several major nucleoid-associated proteins (NAPs) including factor for inversion stimulation (Fis), heat-unstable nucleoid protein (HU), and histone-like nucleoid structuring protein (H-NS) like proteins[2]
We examined the mechanical effects of DNA-binding proteins from starved cells (Dps) and Integration host factors (IHF) binding to a single 48,502 bp λ -DNA using a transverse magnetic tweezers setup revised from that described in our previous work[34] (Fig. 1a)

Summary

Introduction

Bacteria have a genomic DNA with a contour length that can be in the order of millimetre range (e.g. E. coli, Salmonella, etc). Bacteria are frequently exposed to severe environmental changes in pH, temperature, osmolarity and oxidative stress, as well as nutritional deprivation Under these stressful conditions, the nucleoid in bacteria is organized differently by certain NAPs which protect the bacterial genome and regulate transcription in order to survive through these growth-limiting and potentially lethal conditions. During nutritional deprivation, DNA-binding proteins from starved cells (Dps), another NAP, is up-regulated to organize the nucleoid and protect it from diverse damages[7]. Many studies have focused on understanding the nucleoid architecture in the exponential growth phase, where nucleoid is organized by several major NAPs including factor for inversion stimulation (Fis), heat-unstable nucleoid protein (HU), and histone-like nucleoid structuring protein (H-NS) like proteins[2]. The E. coli nucleoid in the exponential growth phase is largely determined by competitive binding of these proteins onto different regions of DNA17,18

Methods

Results

Conclusion